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import visual_behavior_glm
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import visual_behavior_glm.src.GLM_params as glm_params
import visual_behavior_glm.src.GLM_analysis_tools as gat
from visual_behavior_glm.src.glm import GLM
import matplotlib.pyplot as plt
import visual_behavior.data_access.loading as loading
import visual_behavior.database as db
import plotly.express as px
import pandas as pd
import numpy as np
import os
from sklearn.cluster import KMeans
from sklearn.manifold import TSNE
from sklearn.decomposition import PCA
import seaborn as sns
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%matplotlib inline
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get experiments_table¶
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import visual_behavior.data_access.loading as loading
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experiments_table = loading.get_filtered_ophys_experiment_table()
# sessions_table = loading.get_filtered_ophys_session_table()
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expts_with_licks = [984551228, 1010530054, 881949066, 980673831, 1007929142, 933338719]
# 459777_940852658_Camk2a-tTA_VISp_175_OPHYS_3_images_A_CAM2P3
# 480753_984551228_Sst-IRES-Cre_VISp_275_OPHYS_2_images_B_passive_CAM2P3
# 498972_1010530054_Sst-IRES-Cre_VISp_275_OPHYS_2_images_B_passive_CAM2P3
# 435431_881949066_Vip-IRES-Cre_VISp_225_OPHYS_2_images_A_passive_MESO1
# 477202_980673831_Sst-IRES-Cre_VISp_275_OPHYS_2_images_B_passive_CAM2P3
# 495789_1007929142_Sst-IRES-Cre_VISp_275_OPHYS_2_images_A_passive_CAM2P3
# 467951_933338719_Vip-IRES-Cre_VISp_175_OPHYS_2_images_B_passive_CAM2P3
experiments_table.loc[expts_with_licks][['ophys_session_id','cre_line','session_type','equipment_name','exposure_number']]
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get results for glm version 6¶
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results_all = gat.retrieve_results(results_type='full')
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results_all['glm_version'].unique()
#use v4
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rs = gat.retrieve_results(search_dict = {'glm_version': '6_L2_optimize_by_cell'}, results_type='summary')
len(rs)
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rs.keys()
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make a new column called 'identifier' that is {OPHYS_EXPERIMENTID}{CELL_SPECIMEN_ID}. This will give each a unique ID¶
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rs['identifier'] = rs['ophys_experiment_id'].astype(str) + '_' + rs['cell_specimen_id'].astype(str)
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rs
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pivot the table to get it into a form for clustering¶
first get variance explained for full model to filter out poorly fit cells¶
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model_output_type = 'variance_explained'
ve = rs.pivot(index='identifier',columns='dropout',values=model_output_type).reset_index()
ve
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cells_to_include = ve[ve['Full']>0.01].identifier.values
order = np.argsort(ve[ve.identifier.isin(cells_to_include)==True]['Full'])
cell_order = cells_to_include[order]
len(cells_to_include)
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get fraction change in explained variance after dropout of each regressor¶
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rs.keys()
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# model_output_type = 'fraction_change_from_full'
model_output_type = 'adj_fraction_change_from_full'
rsp = rs.pivot(index='identifier',columns='dropout',values=model_output_type).reset_index()
rsp
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tmp = ve.rename(columns={'Full':'varience_explained_full_model'})
rsp = rsp.merge(tmp[['identifier','varience_explained_full_model']], on=['identifier'])
filter out poorly fit cells¶
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# rsp = rsp[rsp.identifier.isin(cells_to_include)==True]
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rs.keys()
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merge in the identifier, cre_line, session_type and equipment_name columns¶
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rs.keys()
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rspm = rsp.merge(rs[['identifier','cell_specimen_id','ophys_experiment_id','cre_line','session_type','imaging_depth','equipment_name','project_code','session_number','exposure_number','container_id']].drop_duplicates(),left_on='identifier',right_on='identifier',how='inner')
rspm
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rspm.keys()
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add a column for session ID (1, 3, 4, or 6)¶
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rspm.session_type.unique()
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# def map_session_types(session_type):
# session_id = session_type[6:7]
# return session_id
# rspm['session_id'] = rspm['session_type'].map(lambda st:map_session_types(st))
# rspm['session_id'].unique()
save feature matrix to disk¶
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# save = False
# if save:
# rspm.to_csv('/allen/programs/braintv/workgroups/nc-ophys/visual_behavior/ophys_glm/fraction_change_var_explained_v_4_L2_fixed_lambda=1_2020.08.09.csv', index=False)
get the column names to use for clustering¶
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cols_for_clustering = [col for col in rspm.columns if col not in ['identifier','cre_line','session_type','equipment_name',
'session_id', 'imaging_depth','project_code','session_number','exposure_number']]
cols_for_clustering = [col for col in cols_for_clustering if col not in ['image0','image1','image2','image3',
'image4','image5','image6','image7',
'visual', 'Full']]
cols_for_clustering = [col for col in cols_for_clustering if 'single' in col]
cols_for_clustering
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len(cols_for_clustering)
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rspm.columns
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cols_for_clustering = [
'single-all-images',
'single-omissions',
'single-pupil',
'single-running',
'single-rewards',
'single-face_motion_energy',
'single-image_expectation',
'single-change',
'single-hits',
'single-misses',
'single-correct_rejects',
'single-false_alarms',
'single-post_lick_bouts',
'single-post_licks',
'single-pre_lick_bouts',
'single-pre_licks',
'single-time',
'single-model_bias',
'single-model_omissions1',
'single-model_task0',
'single-model_timing1D',
]
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len(cols_for_clustering)
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plot feature matrix¶
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rspm[cols_for_clustering]
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feature_matrix = rspm[cols_for_clustering]
fig, ax = plt.subplots(figsize=(6,10))
ax = sns.heatmap(feature_matrix, vmin=-0.5, vmax=0.5, center=0, cmap='RdBu_r', ax=ax, cbar_kws={'label':model_output_type})
ax.set_ylabel('cells')
ax.set_title('GLM feature matrix')
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feature_matrix = rspm.sort_values('varience_explained_full_model').reset_index()[cols_for_clustering]
fig, ax = plt.subplots(figsize=(6,10))
ax = sns.heatmap(feature_matrix, vmin=-0.5, vmax=0.5, cmap='RdBu_r', center=0, ax=ax, cbar_kws={'label':model_output_type})
ax.set_ylabel('cells')
ax.set_title('GLM feature matrix')
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feature_matrix = rspm.sort_values('omissions').reset_index()[cols_for_clustering]
fig, ax = plt.subplots(figsize=(6,10))
ax = sns.heatmap(feature_matrix, vmin=-0.5, vmax=0.5, cmap='RdBu_r', ax=ax, cbar_kws={'label':model_output_type})
ax.set_ylabel('cells')
ax.set_title('GLM feature matrix')
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feature_matrix.dropna()
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# feature_matrix = rspm.sort_values('omissions').reset_index()[cols_for_clustering]
# fig, ax = plt.subplots(figsize=(6,10))
# ax = sns.clustermap(feature_matrix.dropna(), vmin=-0.5, vmax=0.5, cmap='RdBu_r', ax=ax, cbar_kws={'label':model_output_type})
# ax.set_ylabel('cells')
# ax.set_title('clustered GLM feature matrix')
plot single cell feature vectors across sessions¶
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df = rspm[rspm.project_code.isin(['VisualBehavior', 'VisualBehaviorTask1B'])]
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cell_specimen_ids = df.cell_specimen_id.unique()
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cre_lines = df.cre_line.unique()
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matched_cells = [cell_specimen_id for cell_specimen_id in cell_specimen_ids if len(df[df.cell_specimen_id==cell_specimen_id])>=3]
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session_numbers = np.sort(df.session_number.unique())
for cre_line in cre_lines:
nrows = 4
ncols = 8
fig, ax = plt.subplots(nrows,ncols, figsize=(20,20), sharey=True)
ax = ax.ravel()
cre_df = df[df.cell_specimen_id.isin(matched_cells)&(df.cre_line==cre_line)]
cre_df = cre_df.sort_values(by='varience_explained_full_model', ascending=False)
cre_matched_cells = cre_df.cell_specimen_id.unique()
for i,cell_specimen_id in enumerate(cre_matched_cells[:(nrows*ncols)]):
cdf = df[df.cell_specimen_id==cell_specimen_id]
ax[i] = sns.heatmap(data=cdf.set_index('session_number')[cols_for_clustering].sort_values(by='session_number').T,
vmin=-0.5, vmax=0.5, cmap='RdBu_r', square=True, ax=ax[i], cbar=False)
# ax[i].imshow(cdf[cols_for_clustering].values.T, vmin=-0.5, vmax=0.5, cmap='RdBu_r',)
ax[i].set_xlim(-0.5,len(cdf)+0.5)
ax[i].set_xlabel('')
# ax[i].set_xticks(np.arange(0,len(session_numbers),1))
# ax[i].set_xticklabels(session_numbers)
ax[i].set_ylim(-0.5,len(cols_for_clustering)+0.5)
ax[i].set_yticks(np.arange(0.5,len(cols_for_clustering)+0.5,1))
ax[i].set_yticklabels(cols_for_clustering)
# ax[i].set_yticklabels('')
ax[i].set_title('csid: '+str(cell_specimen_id)+'\n '+cdf.session_type.values[0]+'\ndepth: '+str(int(cdf.imaging_depth.mean())), fontsize=10)
# for y in np.arange(0,nrows*ncols,ncols):
# ax[y].set_xlabel('session #', fontsize=10)
# for x in range(nrows):
# ax[(nrows*ncols-x)-1].set_yticks(np.arange(len(cols_for_clustering)))
# ax[(nrows*ncols-x)-1].set_yticklabels(cols_for_clustering, rotation=0)
plt.suptitle(cre_line+' single cell feature vectors\ncolormap is '+model_output_type+' from -0.5 to 0.5', x=0.52, y=1.03, horizontalalignment='center')
fig.tight_layout()
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characterize median change across sessions¶
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df = rspm[rspm.project_code.isin(['VisualBehavior', 'VisualBehaviorTask1B'])]
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fig, ax = plt.subplots(1,3,figsize=(15,7))
for i,cre_line in enumerate(cre_lines):
tmp = df[df.cre_line==cre_line]
ax[i] = sns.heatmap(data=tmp.groupby(['session_number']).median()[cols_for_clustering].T,
ax=ax[i], square=True)
ax[i].set_xlim(-0.5,len(tmp.session_number.unique())+0.5)
ax[i].set_ylim(-0.5,len(cols_for_clustering)-0.5)
ax[i].set_yticks(np.arange(0.5,len(cols_for_clustering)+0.5,1))
ax[i].set_yticklabels(cols_for_clustering);
ax[i].set_title(cre_line)
fig.tight_layout()
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df = rspm[rspm.project_code.isin(['VisualBehavior', 'VisualBehaviorTask1B'])]
for c,cre_line in enumerate(cre_lines):
tmp = df[(df.cre_line==cre_line)]
containers = np.sort(tmp.container_id.unique())
print(cre_line, len(containers))
fig, ax = plt.subplots(4,5, figsize=(20,20))
ax = ax.ravel()
for i,container_id in enumerate(containers):
cdf = tmp[(tmp.container_id==container_id)]
ax[i] = sns.heatmap(data=cdf.groupby(['session_number']).median()[cols_for_clustering].T, ax=ax[i])
ax[i].set_xlim(-0.5,len(cdf.session_number.unique())+0.5)
ax[i].set_ylim(-0.5,len(cols_for_clustering)-0.5)
ax[i].set_yticks(np.arange(0.5,len(cols_for_clustering)+0.5,1))
ax[i].set_yticklabels(cols_for_clustering);
ax[i].set_title(cre_line+' '+str(int(cdf.imaging_depth.mean()))+'\n'+str(container_id))
fig.tight_layout()
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basic characterization¶
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fig, ax = plt.subplots(figsize=(4,4))
ax = sns.scatterplot(data=rspm, x='omissions', y='all-images', hue='cre_line', ax=ax)
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fig, ax = plt.subplots(figsize=(4,4))
ax = sns.scatterplot(data=rspm, x='omissions', y='pupil', hue='cre_line', ax=ax)
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fig, ax = plt.subplots(figsize=(4,4))
ax = sns.scatterplot(data=rspm, x='pupil', y='running', hue='cre_line', ax=ax)
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colors = sns.color_palette()
colors = [colors[0], colors[2], colors[3]]
cre_lines = np.sort(rspm.cre_line.unique())
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for metric in cols_for_clustering:
fig, ax = plt.subplots(figsize=(6,4))
sns.pointplot(data=rspm, x='session_number', y=metric, hue='cre_line', hue_order=cre_lines, palette=colors, ax=ax)
In [59]:
cre_lines = np.sort(rspm.cre_line.unique())
session_numbers = np.sort(rspm.session_number.unique())
cre_line = cre_lines[0]
session_number = session_numbers[0]
In [60]:
def get_colors_for_session_numbers():
reds = sns.color_palette('Reds_r', 6)[::2]
blues = sns.color_palette('Blues_r', 6)[::2]
return reds + blues
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colors = get_colors_for_session_numbers()
# colors = [c[0], c[2], c[3], c[5]]
In [62]:
colors = get_colors_for_session_numbers()
fig, ax = plt.subplots(1,3, figsize=(16, 8))
for i,cre_line in enumerate(cre_lines):
for c,session_number in enumerate(session_numbers):
data = rspm[(rspm.cre_line==cre_line)&(rspm.session_number==session_number)][cols_for_clustering].melt()
ax[i] = sns.pointplot(data=data, x='value', y='variable', ax=ax[i], color=colors[c], )
ax[i].set_title(cre_line)
plt.legend(labels=session_numbers)
fig.tight_layout()
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# g = sns.PairGrid(rspm[cols_for_clustering+['cre_line']], hue="cre_line")
# g.map_diag(plt.hist)
# g.map_offdiag(plt.scatter)
# g.add_legend();
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PCA on the feature matrix¶
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data = rspm.dropna()
n_features = len(cols_for_clustering)
n_components = len(cols_for_clustering)
pca = PCA(n_components=n_components)
pca_result = pca.fit_transform(data[cols_for_clustering].values)
data['pc1'] = pca_result[:,0]
data['pc2'] = pca_result[:,1]
data['pc3'] = pca_result[:,2]
print('Explained variation per principal component: {}'.format(pca.explained_variance_ratio_))
plot explained variance for PCs¶
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np.cumsum(pca.explained_variance_ratio_)
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np.searchsorted(np.cumsum(pca.explained_variance_ratio_), .90)
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np.searchsorted(np.cumsum(pca.explained_variance_ratio_), .95)
Out[71]:
In [72]:
fig,ax=plt.subplots()
ax.plot(
np.arange(n_components),
pca.explained_variance_ratio_,
'o-k'
)
ax.set_xlabel('PC number')
ax.set_ylabel('variance explained')
ax.set_title('first 12 PCs explain >95% of the variance')
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what are the PCs?¶
In [73]:
fig, ax = plt.subplots(figsize=(6,6))
ax = sns.heatmap(pca.components_, vmin=-1, vmax=1, cmap='RdBu_r', ax=ax, square=True,
robust=True, cbar_kws={"drawedges": False, "shrink": 0.7, "label": 'weight'})
ax.set_ylabel('principal components')
ax.set_xlabel('features')
# ax.set_title('principal axes in feature space \n(directions of maximum variance in the data)')
ax.set_ylim(0, n_components)
ax.set_xticklabels(cols_for_clustering, rotation=90);
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pca.components_.shape
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In [75]:
fig,ax=plt.subplots(figsize=(12,4))
N_PCs = 8
for PC in range(N_PCs):
ax.plot(pca.components_[PC,:])
ax.legend(np.arange(N_PCs), title='PC', bbox_to_anchor=(1,1))
ax.axhspan(1/np.sqrt(32), -1/np.sqrt(32), zorder=-np.inf, alpha=0.25)
ax.set_xticks(np.arange(len(cols_for_clustering)))
ax.set_xticklabels(cols_for_clustering, rotation=45, ha='right')
ax.set_ylabel('weight')
ax.set_ylim(-1.1,1.1)
fig.tight_layout()
In [77]:
fig,ax=plt.subplots(figsize=(12,4))
for PC in range(8,20):
ax.plot(pca.components_[PC,:])
ax.legend(np.arange(10,21), title='PC', bbox_to_anchor=(1,1))
ax.axhspan(1/np.sqrt(32), -1/np.sqrt(32), zorder=-np.inf, alpha=0.25)
ax.set_xticks(np.arange(len(cols_for_clustering)))
ax.set_xticklabels(cols_for_clustering, rotation=45, ha='right')
ax.set_ylabel('weight')
ax.set_ylim(-1.1,1.1)
fig.tight_layout()
plot covariance matrix¶
In [80]:
fig, ax = plt.subplots(figsize=(6,6))
ax = sns.heatmap(pca.get_covariance(), vmin=-0.08, vmax=0.08, cmap='RdBu_r', ax=ax, square=True,
robust=True, cbar_kws={"drawedges": False, "shrink": 0.7, "label": 'covariance'})
ax.set_title('covariance matrix')
ax.set_ylim(0, n_features)
ax.set_xticklabels(cols_for_clustering, rotation=90);
ax.set_yticklabels(cols_for_clustering, rotation=0);
plot PCA result¶
In [81]:
pca_result[np.argsort(pca_result[:,0])]
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In [82]:
fig, ax = plt.subplots(figsize=(6,10))
ax = sns.heatmap(pca_result, cmap='RdBu_r', ax=ax,
robust=True, cbar_kws={"drawedges": False, "shrink": 0.7, "label": 'activation'})
ax.set_ylabel('cells')
ax.set_xlabel('PC')
ax.set_title('% variance explained in PC space')
ax.set_ylim(0, pca_result.shape[0])
ax.set_xlim(0, pca_result.shape[1])
ax.set_xticks(np.arange(0, pca_result.shape[1]));
# ax.set_xticklabels(cols_for_clustering, rotation=90);
In [83]:
fig, ax = plt.subplots(figsize=(6,10))
ax = sns.heatmap(pca_result[np.argsort(pca_result[:,0])], cmap='RdBu_r', ax=ax,
robust=True, cbar_kws={"drawedges": False, "shrink": 0.7, "label": 'activation'})
ax.set_ylabel('cells')
ax.set_xlabel('PC')
ax.set_title('% variance explained in PC space')
ax.set_ylim(0, pca_result.shape[0])
ax.set_xlim(0, pca_result.shape[1])
ax.set_xticks(np.arange(0, pca_result.shape[1]));
# ax.set_xticklabels(cols_for_clustering, rotation=90);
plot data in PC space¶
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In [84]:
# pc1 and pc2 columns in rspm correspond to pca_results for those PCs - is this the 'score' per cell?
fig,ax = plt.subplots(1,2,figsize=(12,6))
ax[0] = sns.scatterplot(data=data, x="pc1", y="pc2", hue="cre_line",
palette=sns.color_palette("hls", 3), legend="full", alpha=0.3, ax=ax[0])
# ax[0].set_xlim(-5,10)
# ax[0].set_ylim(-5,10)
ax[1] = sns.scatterplot(data=data, x="pc2", y="pc3", hue="cre_line",
palette=sns.color_palette("hls", 3), legend="full", alpha=0.3, ax=ax[1])
# ax[1].set_xlim(-5,10)
# ax[1].set_ylim(-5,10)
In [85]:
pca_result_df = pd.DataFrame(pca_result, index=data.identifier)
pca_result_df['cre_line'] = data['cre_line'].values
In [86]:
# pc1 and pc2 columns in rspm correspond to pca_results for those PCs - is this the 'score' per cell?
PC1 = 0
PC2 = 1
PC3 = 3
PC4 = 4
fig,ax = plt.subplots(1, 3, figsize=(15,5))
ax = ax.ravel()
i=0
ax[i] = sns.scatterplot(data=pca_result_df, x=PC1, y=PC2, hue="cre_line",
palette=sns.color_palette("hls", 3), legend="full", alpha=0.3, ax=ax[i])
# ax[i].set_xlim(-100,100)
# ax[i].set_ylim(-100,100)
i+=1
ax[i] = sns.scatterplot(data=pca_result_df, x=PC2, y=PC3, hue="cre_line",
palette=sns.color_palette("hls", 3), legend="full", alpha=0.3, ax=ax[i])
# ax[i].set_xlim(-100,100)
# ax[i].set_ylim(-100,100)
i+=1
ax[i] = sns.scatterplot(data=pca_result_df, x=PC3, y=PC4, hue="cre_line",
palette=sns.color_palette("hls", 3), legend="full", alpha=0.3, ax=ax[i])
# ax[i].set_xlim(-100,100)
# ax[i].set_ylim(-100,100)
fig.tight_layout()
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In [88]:
query_string = '''pc1>-100 and pc1<100 and pc2>-100 and pc2<100 and pc3>-100 and pc3<100'''
fig = px.scatter_3d(
data.query(query_string),
x='pc1',
y='pc2',
z='pc3',
color='cre_line',
)
fig.update_traces(
marker=dict(
size=3,
opacity=0.25
)
)
fig.update_layout(
margin=dict(l=30, r=30, t=10, b=10),
width=1200,
height=1000,
)
# fig.write_html("/home/dougo/code/dougollerenshaw.github.io/figures_to_share/2020.08.09_PCA_on_GLM.html")
# fig.show()
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In [89]:
# # pc1 and pc2 columns in rspm correspond to pca_results for those PCs - is this the 'score' per cell?
# fig,ax = plt.subplots(n_components, n_components, figsize=(20,20))
# ax = ax.ravel()
# i = 0
# for PC1 in range(n_components):
# for PC2 in range(n_components):
# ax[i] = sns.scatterplot(data=pca_result_df, x=PC1, y=PC2, hue="cre_line",
# palette=sns.color_palette("hls", 3), legend="full", alpha=0.3, ax=ax[i])
# ax[i].set_xlim(-100,100)
# ax[i].set_ylim(-100,100)
# # ax[1] = sns.scatterplot(data=rspm, x="pc2", y="pc3", hue="cre_line",
# # palette=sns.color_palette("hls", 3), legend="full", alpha=0.3, ax=ax[1])
# # ax[1].set_xlim(-100,100)
# # ax[1].set_ylim(-100,100)
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cluster with k-means¶
cluster on feature matrix¶
In [90]:
feature_matrix = data[cols_for_clustering]
fig, ax = plt.subplots(figsize=(6,10))
ax = sns.heatmap(feature_matrix, vmin=-0.5, vmax=0.5, cmap='RdBu_r', ax=ax, cbar_kws={'label':model_output_type})
ax.set_ylabel('cells')
ax.set_title('GLM feature matrix')
Out[90]:
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### need to add Doug's code for sorting feature matrix by cluster ID
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cluster on PCA results¶
In [95]:
fig, ax = plt.subplots(figsize=(6,10))
ax = sns.heatmap(pca_result, cmap='RdBu_r', ax=ax,
robust=True, cbar_kws={"drawedges": False, "shrink": 0.7, "label": 'weight'})
ax.set_ylabel('cells')
ax.set_xlabel('PC')
ax.set_title('')
ax.set_ylim(0, pca_result.shape[0])
ax.set_xlim(0, pca_result.shape[1])
ax.set_xticks(np.arange(0, pca_result.shape[1]));
# ax.set_xticklabels(cols_for_clustering, rotation=90);
In [97]:
kmeans = KMeans(n_clusters=10)
kmeans_result = kmeans.fit_predict(pca_result)
data['kmeans_result'] = kmeans_result
data['kmeans_result'].value_counts()
Out[97]:
"Then we applied consensus clustering to the PCs, by running K-means using the PCs 100 times until reaching a stable co-clustering association matrix, where each entry represents the probability of two units belonging to the same cluster." - Xiaoxuan paper
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try seaborn clustermap¶
In [99]:
# tmp = data.copy()
# cre_lines = tmp.pop('cre_line')
# lut = dict(zip(cre_lines.unique(), "rbg"))
# row_colors = cre_lines.map(lut)
# ax = sns.clustermap(data[cols_for_clustering], cmap='RdBu_r', row_colors=row_colors)
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